GemCell:
A Generic Platform for Modeling Multi-Cellular Biological Systems

Hila Amir-Kroll, Avital Sadot, Irun R. Cohen and David Harel

The mass and complexity of biological information requires computer-aided simulation and analysis to help scientists
achieve understanding and guide experimentation. Although living organisms are composed of cells, actual genomic
and proteomic data has not yet led to a satisfactory model of working cell in-silico. We have set out to devise a
user-friendly generic platform, GemCell, for Generic Executable Modeling of Cells, based on whole, functioning cells.
Starting with the cell simplifies life, because all cells expresses essentially five generic types of behavior: replication,
death, movement (including change of shape and adherence), export (secretion, signaling, etc.) and import (receiving
signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for particular kinds
of cells as part of a database of biological specifics (the DBS), which specifies the cell properties and functions that
depend on the cell’s history, state, environment, etc. The DBS is designed in an intuitive fashion, so users are able to
easily insert their data of interest. The generic part of GemCell, built using Statecharts, is a fully dynamic model of a
cell, its interactions with the environment and its resulting behavior, individually and collectively. Model specificity
emerges from the DBS, so that model execution is carried out by the statecharts executing with the aid of specific
data extracted from the DBS dynamically. Our long term goal is for GemCell to serve as a broadly applicable
platform for biological modeling and analysis, supporting user-friendly in-silico experimentation, animation,
discovery of emergent properties, and hypothesis testing, for a wide variety of biological systems.

Structure of GemCell: The GemCell model is a combination of
generic biology, formed by five generic laws of inter-cellular behavior,
and specific biology, built from the data of actual cellular systems.
GemCell consists of three components: the generic state-based model,
which models the generic biology; the DBS, which holds the information
about the specific cellular system that the user wishes to model;
and the output of the system’s dynamics that emerges from the execution
of the generic model combined with the DBS. These three components
are integrated and operate together continuously during model execution.


* See full paper in :
H. Amir-Kroll, A. Sadot, I.R. Cohen and D. Harel,
"GemCell: A Generic Platform for Modeling Multi-Cellular
 Biological Systems", Electronic Notes in Theoret. Comput. Sci.,
 in press.